Hello damuehlbauer,
[Topice moved here.]
It isn't possible for any given combination to have two different stored registrations.
My first guess is that you had actually assigned the computer key to trigger a different combination piston from the one you intended.
Please first make sure that SET and SCOPE modes are both turned off (on the Registration large control panel, for example), then right-click on the virtual combination button/piston, select 'Auto-detect ...' and auto-detect it to the relevant computer key, then click the Done button on the auto-detection screen.
Does the computer key then trigger the same registration as clicking on specifically the virtual piston that you auto-detected the computer key to? It should.
(Please note also that Hauptwerk's 'master generals' are usually *separate* combinations from any generals that a sample set producer might have included on the virtual console.)